Friday, July 29, 2011

Positive Results and Technology in the Classroom

After 3 weeks of moving in fits and starts, we hit our stride this week. We were able to build a surface monolayer of thiol on our gold substrate and test it using FTIR. The peaks showed up with the proper intensity and position, so we feel confident that we can move on (My takeaway lesson from this is to get a good set of instructions early on so you are not reinventing the wheel). Next week, our last week of experimenting, will involve creating a concentration curve to determine the concentration where the monolayer starts to show incomplete packing. This will be valuable for the research group because it will minimize the material required to do experiments and add to the overall understanding of the system.

Our seminar today was on implementing technology in the classroom. In my short time as an educator, I have gone through many similar discussions, all with the theme "USE TECHNOLOGY!" However, more often than not, the suggestions would be impractical or laughably low-tech (Powerpoint?). Today's seminar was a refreshing change of pace. Our presenter was well informed and took us beyond the normal Teachertube/blog entry points. The most interesting site she showed us was, a site that allows you to post interactive movies/lessons/etc. I have wanted to podcast lectures this year, and this site will allow me to do this with ease. Students will then have a chance to post replies directly to me and/or make their own video/photo response. Direct implications for my teaching = yeah!

Thursday, July 21, 2011

50% Already?

It is hard to believe that tomorrow will mark the midpoint of the summer RET experience. Time flies when you are having fun!

I spent the morning at home today, combining video clips I had made about the experience into a single movie. I hope it gives a little feel to the research we are doing and what it is like to be an engineer. Sadly, my direction and editing doesn't do it justice: research is exciting.

Today was also special because my family came in to visit the Photonics center. Here is a picture of me with my son in our lab. It's never too early to start training the next generation!

In terms of our experiments, we have been gathering a lot of data, but it has been... inconclusive. Our monolayer thicknesses are low, but close to what is expected. Our FTIR analysis shows the peaks we are looking for, but not with the magnitudes we expect.

So what do we do?

Solving problems like this is where an engineer earns her or his salary.

We have decided to take a dual pronged approach. We are going to move forward with some of the chips that we have made and add the final layer. We can then test with the ellipsometer and FTIR to get an idea of how the bonding went. It MAY be that we have sufficient covering of the chip (despite our mediocre results). While doing this, we will also be testing different thiol solution concentrations. The thought being that if we soak the chips in a high molarity solution, we might get better bonding on the gold surface (and thus a better gold monolayer). We should have some preliminary results as soon as tomorrow and from there, we will analyze the data and make decisions about future experiments.

Thursday, July 14, 2011

The Reality of Research

As you get farther away from life experiences, certain specifics tend to fade. The big lessons remain, but some of the details drop from the forefront. It has been 3 years since I have worked in a research lab and the idea of how to do research is still fresh (hammered home by an excellent lecture by Dr. Selim Unlu this week), but the ease with which projects can be delayed slipped from my memory. I often tell my students that science requires patience and my partner and I have had to exercise our own this week.

In our quest to create a multi-layered chip that can be used to detect viruses and proteins, we have hit a series of minor roadblocks. Our first thiol monolayer experiment appeared to go smoothly. Theoretically, it should look something like this (the red represents the sulfur group):

(image from

But the question is, how can we determine if this actually happened? The molecules are so small that we have no method to actually see them aligned as they are above, so we need to measure them indirectly. The first way we do this is using an ellipsometer. This apparatus measures the change in polarization of light after it is reflected off of a surface. This change, when coupled with a refractive index, can give you the thickness of the deposited layer. Our results came out to be a reasonable 1 nm (to give some perspective on the size, 1 nm is to the thickness of a human hair as 1 football field is to the distance between New York and Los Angeles). So we were confident that we could add layers 2 and 3. I will delve into more depth about these layers in future entries, but they will end up being used to bond the antibody of interest to our surface. The application process went smoothly, but when we went to check the new thickness of the ellipsometer, we ran into speedbump #1. The ellipsometer was down and the one person who could help us was out of the office. I had forgotten how frequently this happens in research, but instead of getting frustrated, we used the time to do more background reading on the topic. The delay allowed me to become more knowledgeable about my topic. With our short timeline, we feel rushed to move forward, but we forget that it is better to gather all information at each step in the process.

Speedbump #2 is getting trained on the FTIR (Fourier Transform - Infrared Spectrometer). While the ellipsometer tells you the thickness of the layer, it doesn't identify what is on the surface. We use the FTIR to tell use exactly what is on the surface (though it doesn't tell us the thickness, so we need both measurements to be sure). The FTIR is a complex machine, but in short, it emits a beam of infrared light onto the sample. The sample absorbs specific wavelengths depending on the bonds that it contains. The FTIR reads this absorbance pattern and can help us determine what we have. As is common with many analytical devices, it is tricky to use, so we need expert training (which we will get next week). Once this training is completed, we can test our chips to confirm that we have deposited the material correctly.

These 2 delays aside, the experimental plan is coming together nicely. Our first testable question is "Does our procedure provides consistent samples?. If we are successful, as judged by our ellipsometer and FTIR results, we will move on to "Can our chip be used to capture a specific protein?" This will involve a new set of tests, with a new set of vocabulary, but it is exciting to think of the possibilities!

Tuesday, July 12, 2011

Getting Work Done!

We made something yesterday.

In fact, we made 2 somethings!

We spent the morning in the clean room, a place where we have to wear layers of clothing, not to protect us, but to protect the equipment from our skin/hair/bodily dirt. Microchips are in all of our electronic devices, and this is the environment where they are made/researched.

Our first step in the clean room was to take a glass wafer (basically a piece of glass) and spin a chemical on it. The chemical is called photoresist and is made up of a material that is sensitive to certain light. After we put on the photoresist the chip was heated for about 1 minute (called the "soft bake") and placed in a machine to expose the photoresist. The machine contains a mask (which can be thought of as a stencil) and only the areas where light passes through are exposed. The light reacts with the photoresist to create a new substance with different chemical properties. This means that it cannow be put in a solvent that will selectively remove the area that was exposed (or, in some cases, the areas that weren't exposed). After removing the exposed areas in the solvent, we could see some of the features that were made. The chips were then stored for future use.

I went first, and made some mistakes... Below is my first chip where the photoresist was not spread equally (though it is hard to see the imperfections). This means that there are areas of different thickness, which can cause problems down the road. The second chip came out better, hopefully it will work as we move forward.

In the afternoon, my partner Valentina and I tried to make our first monolayer of thiol on gold (which is part of our main project). It started slowly (we needed to call Carlos, our post doc leader, to find out where the vials were... which is the absolute first step in the process). But from there we were pretty independent. We will analyze the chips today to determine if we did it correctly. Is it okay that I'm nervous?

Below is a picture of the chips as they were being cleaned.

Friday, July 8, 2011

End of Week 1

After my first full week on the job, I feel like I'm finally starting to get acclimated to the new environment. I have access to the necessary rooms, all of the computer logistics have been solved, and I have gowned up and gone into the clean room a whopping 3 times! Everyone has been wonderful to work with and very supportive, I'm glad I chose to spend the summer here (plus the view from my lab is amazing).

Now, onto the science!

Since the project is new to me, I'm not yet confident with the specifics. However, here is my current understanding of what we will be working on: We are applying multiple layers of molecules to chips in order to detect small quantities of proteins and viruses. Specifically, I will be working with another RET (Valentina Sountsova) and grad students/post docs on applying thiols to a gold-coated wafer. These thiols will arrange on the surface with the sulfur functional group bonding with the gold. This leaves carboxyl groups organized nicely on the open end. This carboxyl will then react with a protein/antibody that has a receptor specific to our compound of interest. The goal is to be able to use light to measure the thickness of the layer of materials to see how much of the virus has been bound to the surface.

I am excited to see how my knowledge will expand in the coming weeks so I can refine this understanding :)

We have been lucky enough to get a few hands-on experiences already. The first was our trip clean room. The two areas are designated class-1000 (less than 1000 particles per cubic foot) and class-100 (less than 100 particles per cubic foot... we have to be extra careful in this room). This level of cleanliness is required for much of the processing of the chips we are working with.

Here is a picture of one of the class-1000 rooms.

We also learned the steps involved in bonding different thiols with our gold chip (I must say, all this talk of gold makes me feel like we are working with untold riches, however the layer of gold is so thin that it has no resale value). This is a multi-step process that requires an entire night to react completely. A particularly interesting step required us to clean the gold surface using a substance called "Piranha Cleaner", 3 parts sulfuric acid to 1 part hydrogen peroxide. I had visions of little fish attacking all of the residual organics on the surface. Munch Munch. Jokes aside, this is not something you want to mess around with. You can see the work station below.

Finally, we learned 2 types of measurements; ellipsometry and FTIR. I understand some of the basics, but will save a more detailed explanation until we start getting some results.

All in all, it was an eventful first week and I look forward to what the next 5 weeks will bring!

Wednesday, July 6, 2011

Back in the Lab

Welcome to my first Research Experience for Teachers (RET) blog posting. I hope to use this site to reflect on my experiences in the program, connect the science to my chemistry curriculum, and to share some of the exciting work I will be doing.

This summer will see me spending 6 weeks at BU studying biophotonics. The research will be done primarily in the Photonics building, a beautiful facility that has an incredible amount of state-of-the-art equipment. Below is a picture of the building as seen from Cambridge (photo from

I come into this program with a different background than many of my colleagues. I worked in biotechnology for 5 years before coming to teaching. My specialty was in pulmonary delivery of medications, but my training was broad enough to touch on many of the topics that are being studied in the photonics building. This has allowed me to have a vague idea about what the faculty are talking about, but the specifics remain illusive.

It is this last point that excites me the most. It may seem strange to be enthusiastic about one's own ignorance, but the quest to connect disparate shards of knowledge with new information to form novel understandings is at the heart of education. This will be the first time that I will be studying "new" science since I left industry and now I come at the process with a different view. The question isn't "How can this idea be used to make money?" , but "How do I introduce this idea to my students to increase understanding and get them excited about science?" I'm excited for the journey (and for the opportunity to get my hands dirty again).